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samtools-software [2019/09/03 22:00] – aorthsamtools-software [2021/01/17 10:22] – aorth
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 samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
  
-  * Latest Version: 1.9+  * Latest Version: 1.11
   * Added: February, 2015   * Added: February, 2015
-  * Updated: September, 2019+  * Updated: January, 2021
   * Link: http://www.htslib.org   * Link: http://www.htslib.org
  
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 <code>$ module avail samtools</code> <code>$ module avail samtools</code>
  
-Load a particular version of samtools:+Load a particular version of samtools into your environment and run it:
  
-<code>$ module load samtools/1.9</code>+<code>$ module load samtools/1.11 
 +$ samtools</code>
  
 ===== Installation ===== ===== Installation =====
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 +$ wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 
-$ tar xf samtools-1.9.tar.bz2 +$ tar xf samtools-1.11.tar.bz2 
-$ cd samtools-1.9+$ cd samtools-1.11
 # install a newer compiler from Red Hat software collections # install a newer compiler from Red Hat software collections
 $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
 $ scl enable devtoolset-7 bash $ scl enable devtoolset-7 bash
-$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.9 --with-htslib=/export/apps/htslib/1.9+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.11 --with-htslib=/export/apps/htslib/1.11
 $ make $ make
-$ sudo mkdir -p /export/apps/samtools/1.9 +$ sudo mkdir -p /export/apps/samtools/1.11 
-$ sudo chown aorth /export/apps/samtools/1.9+$ sudo chown aorth /export/apps/samtools/1.11
 $ make install $ make install
-$ sudo chown -R root:root /export/apps/samtools/1.9</code>+$ sudo chown -R root:root /export/apps/samtools/1.11</code>
  
-This links against htslib installed as a module in htslib/1.9.+This links against htslib/1.11, which is installed as a module.
samtools-software.txt · Last modified: 2022/06/23 09:35 by aorth